As the process starts at EMERGE, you have to set up the Markup Fee at this stage.

Open the Integration module, and click the SETTINGS button of Stripe or Airwallex.

In the CONFIGURATION, click EDIT to set up the account information.

At Percentage markup applied to the Invoice amount, choose "Add markup" and enter the percentage you need to charge customers. Remember to Connect when you're done.

Once the setup is complete, the invoice PDF document will have a Payment link line with the associated markup fee as shown below.